tuple index out of range error

[mja]

When running the command

python PGxPOP/bin/PGxPOP.py --vcf chr10_HRC.vcf.gz --gene CYP2C19 --phased --build hg19 --batch --output cyp2c19 

I'm getting the error

Traceback (most recent call last):
  File "PGxPOP/bin/PGxPOP.py", line 308, in <module>
    cd.run()
  File "PGxPOP/bin/PGxPOP.py", line 54, in run
    results = self.process_gene(g)
  File "PGxPOP/bin/PGxPOP.py", line 68, in process_gene
    diplotypes, sample_variants, uncallable = self.get_calls(gene, gt_matrices)
  File "PGxPOP/bin/PGxPOP.py", line 177, in get_calls
    for samp in range(gt_mat[0].shape[1]):
IndexError: tuple index out of range

Here is a gist with the --debug output.

Is it possibly because not all of the variants are in the VCF file?

[mja]

OK, I think I've gotten it to run by not using the --batch argument.